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<p>Hi Basil</p>
<p>I am attaching the outcome from the ctf refinement. Thank you very much for your help.</p>
<p>Best regards<br>
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<div id="divRplyFwdMsg" dir="ltr"><font color="#000000" face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b> Basil Greber <basilgreber@gmx.net><br>
<b>Sent:</b> Sunday, May 3, 2020 6:50 PM<br>
<b>To:</b> Mohamed A Sayed<br>
<b>Cc:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> Re: [3dem] question in post-processing</font>
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<div>Hi Mohamed,
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<div>Have you done CTF refinement, beam tilt in particular?</div>
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<div>Basil</div>
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<div>Am 03.05.2020 um 07:37 schrieb Mohamed A Sayed <<a href="mailto:mohamed.sobhy@kaust.edu.sa">mohamed.sobhy@kaust.edu.sa</a>>:</div>
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<span style="font-size:12pt">Hello,</span></div>
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<div style="margin-top:0px; margin-bottom:0px">I hope all is safe. If you would please advise on the following:</div>
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<div style="margin-top:0px; margin-bottom:0px">I made auto-refinement for a structure u<span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">sing auto-sampling settings: I</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">nitial
angular sampling</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)"> 3.</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">7,
local searching from auto-sampling 1.8. T</span>he output after convergence<span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)"> was "Final resolution (without masking) is: 3.26154</span>)". When I
generate a mask using binarisation threshold from 0.001 to 0.005, where 0.005 gave warning, the FSC curve has a prominent peak in the FSC plot. I tried changing these parameters and tried the output from other refinement job with bigger box but all give this
peak.<br>
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<div style="margin-top:0px; margin-bottom:0px">my questions<br>
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<div style="margin-top:0px; margin-bottom:0px">1- What caused and how to get rid of this peak?<br>
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<div style="margin-top:0px; margin-bottom:0px">2- If this peak problem could not be fixed, can I use proceed with such post-process.star file for ctf refinement and polishing?</div>
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<div style="margin-top:0px; margin-bottom:0px">Thank you very much for your help and time. <br>
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<div style="margin-top:0px; margin-bottom:0px"><span id="cid:856f3e94-8d33-4343-b90c-0da81494cd59"><pastedImage.png></span><br>
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<div style="margin-top:0px; margin-bottom:0px">Last iteration before conversion: <br>
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<div> CurrentResolution= 3.93402 Angstroms, which requires orientationSampling of at least 2.04545 degrees for a particle of diameter 220 Angstroms</div>
<div> Oversampling= 0 NrHiddenVariableSamplingPoints= 1305</div>
<div> OrientationalSampling= 0.46875 NrOrientations= 145</div>
<div> TranslationalSampling= 0.4605 NrTranslations= 9</div>
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<div> Oversampling= 1 NrHiddenVariableSamplingPoints= 41760</div>
<div> OrientationalSampling= 0.234375 NrOrientations= 1160</div>
<div> TranslationalSampling= 0.23025 NrTranslations= 36<br>
<span style="font-size:12pt">E</span><span style="font-size:12pt">xpectation iteration 25</span><br>
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<span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none; float:none; display:inline!important">3dem
mailing list</span><br style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none">
<a style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; background-color:rgb(255,255,255)" href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a><br style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none">
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